MmuINT0140498 @ mm10
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26429062-26429516:-
Coord C1 exon
chr2:26429374-26429516
Coord A exon
chr2:26429124-26429373
Coord C2 exon
chr2:26429062-26429123
Length
250 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACC
5' ss Score
8.55
3' ss Seq
CTCTGCCCCTCTTGTTGCAGACC
3' ss Score
11.23
Exon sequences
Seq C1 exon
TTCCATCAAGACCGACCTCTCCTGAGAAGTTTACGGTGCCTCATGTCTGTGCCAGGTTTGGTCCTGGTGGTCAGCTCCTTAAAGTGATTCCCAACCTGCCTTCAGAAGGACAGCCTGCACTGGTGGAGATCCACAGCTTAGAG
Seq A exon
GTAACCATGGGTCTGTGGTGCTGTCGGTACCCCATGGCCTTGGAAAACATGCTTCCATGAAAAGCTCAGGTTTATAGGGCTTTGGTTTAAAGTTGGAAAATCTCCATTGGAGTCCATGCTCATGTAATTGTACCAAGTACCTTCACACTCTGGGTAGAGGGGTGGGTGTGGTTCCAGAAATGGTTTTTGTGACTCAGTCTGCCAGAGGTTCGGACTGCACACATGACCCACTCTGCCCCTCTTGTTGCAG
Seq C2 exon
ACCTTGCTGCAGCACACACCTGAGCAGGAAGAGATGCGCTCCTTCCCAGGACCTCTCGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924:ENSMUST00000114082:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.321 A=NA C2=0.876
Domain overlap (PFAM):
C1:
PF129322=Sec16=PU(33.0=70.8)
A:
NA
C2:
PF129322=Sec16=FE(19.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATCAAGACCGACCTCTCCT
R:
CGAGAGGTCCTGGGAAGGAG
Band lengths:
199-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types